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- PDB-3fhr: High resolution crystal structure of mitogen-activated protein ki... -

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Basic information

Entry
Database: PDB / ID: 3fhr
TitleHigh resolution crystal structure of mitogen-activated protein kinase-activated protein kinase 3 (MK3)-inhibitor complex
ComponentsMAP kinase-activated protein kinase 3
KeywordsTRANSFERASE / Kinase-inhibitor complex / ATP-binding / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


macropinocytosis / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / mitogen-activated protein kinase binding / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation ...macropinocytosis / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / mitogen-activated protein kinase binding / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation / VEGFA-VEGFR2 Pathway / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...MAP kinase activated protein kinase, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-P4O / MAP kinase-activated protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCheng, R.K.Y. / Barker, J. / Palan, S. / Felicetti, B. / Whittaker, M. / Hesterkamp, T.
CitationJournal: Protein Sci. / Year: 2010
Title: High-resolution crystal structure of human Mapkap kinase 3 in complex with a high affinity ligand
Authors: Cheng, R. / Felicetti, B. / Palan, S. / Toogood-Johnson, I. / Scheich, C. / Barker, J. / Whittaker, M. / Hesterkamp, T.
History
DepositionDec 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAP kinase-activated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9152
Polymers38,5751
Non-polymers3401
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.688, 74.832, 60.664
Angle α, β, γ (deg.)90.00, 107.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MAP kinase-activated protein kinase 3 / Mitogen-activated protein kinase-activated protein kinase 3 (MK3) / MAPK-activated protein kinase 3 ...Mitogen-activated protein kinase-activated protein kinase 3 (MK3) / MAPK-activated protein kinase 3 / MAPKAP kinase 3 / MAPKAPK-3 / Chromosome 3p kinase / 3pK


Mass: 38574.980 Da / Num. of mol.: 1 / Fragment: Kinase domain, UNP residues 33-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: Q16644, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-P4O / 2-(2-QUINOLIN-3-YLPYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE


Mass: 340.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10%-15% PEG 3350, 100mM BisTris propane/citric acid, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: double Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 1.9→31.43 Å / Num. obs: 27952 / % possible obs: 97.9 % / Redundancy: 3.37 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.7 / % possible all: 85

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.298 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.324 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1423 5.1 %RANDOM
Rwork0.2258 ---
obs0.22809 26526 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.762 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å20 Å2-0.27 Å2
2---2.31 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 26 108 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222300
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9683110
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41724.505111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09915416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2331513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021736
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21141
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21529
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2159
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9731.51409
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64822210
X-RAY DIFFRACTIONr_scbond_it2.21131026
X-RAY DIFFRACTIONr_scangle_it3.3424.5898
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 83 -
Rwork0.379 1681 -
obs--83.48 %

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